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Assign snps to clumps based on LD after gwas

snp_make_clumps.Rd

Assign snps to clumps based on LD after gwas

Usage

snp_make_clumps(
  geno.bed.filename,
  geno.bed.dir,
  gwas.res,
  pvals.in.log = T,
  window = 500,
  ld.thresh = 0.5,
  plink.path = NULL,
  out.dir = NULL
)

Arguments

geno.bed.filename

character, filename of genotype bedfile, no .bed extension

geno.bed.dir

character, path to directory where bed/bim/fam files exist, include trailing "/"

gwas.res

data.frame, table of gwas results with columns (marker.ID, CHR, POS, PVAL)

pvals.in.log

boolean, are pvalues in gwas.res in -log10(p) or not

window

integer, window in kilobases either side of snp to look for snps in LD,

ld.thresh

numeric, R2 threshold above which snps will be grouped

path to plink 2 executable

out.dir

character, path to a temporary directory to output some intermediate files

Value

table with columns marker.ID and clump_num. Clump_num indicates groupings, numberings start from the larges pvalue to smallest. May want to reassign afterwards to be along the genome.

Examples

# work in progress